Damjan,
can you recommend any downloadable 16bit app that stresses the MCI?
It's good that you noticed that RECT16 and RECT do not have the same size (whack!). Yet I'm surprised that you left MCI_WINDOW untouched. I believe that the apps that use MCI_WHERE/PUT etc. (i.e. MCIAVI) are likely to use MCI_WINDOW as well to set the window handle.
Does no FIXME appear in your console? http://source.winehq.org/source/dlls/mmsystem.dll16/mci16.c#L182 The comment there is obsolete. dwFlags is available and could be used like I did in db0df4c067fd6b701905aaef735c4729fca9d73f
Regards, Jörg Höhle